Analysis of Protein Intramolecular and Solvent Bonding on Example of Major Synovial Fluid Component

Molecular interactions within proteins are fundamental to maintain their conformation and role in biological systems. Understanding the nature and dynamics of the interactions is crucial as it can help understand phenomena occurring during physiological processes, drug design, and delivery, etc. This chapter presents the analysis of the dynamics of molecular interactions inside proteins on an example of albumin. We have performed computer simulations of albumin protein at its native/equilibrium state to understand the dynamics of bonding/interactions inside the protein and with water: hydrogen bonds and hydrophobic interactions. Furthermore, we extracted the data to look into interactions between particular amino acids (AA). As expected, charged AA, such as the glutamic acid (GLU) and lysine (LYS) one, form most intermolecular hydrogen bonds and bind most water.

Further, in hydrophobic contacts, the significant role plays phenylalanine (PHE) and leucine (LEU) amino-acids. We have also found that although its hydrophobic nature, the LEU forms the most stable contacts. This can be attributed to its position in the core of the protein. The presented results may help better understand the dynamics of a complex structure such as protein.